Metal Gear 2: Solid Snake: Great need for a new power source leads to the development of the algae OILIX. Unfortunately, as it is usually the case, the inventor of the new source is kidnapped by soldiers of Zanzibar Land and their leaders, claiming they will hold the world hostage with this new source and their nuclear arsenal. Solid Snake is brought out of retirement to infiltrate Zanzibar Land and rescue the scientist responsible for OILIX's creation.

Solid Snake's mission received a monkey wrench the size of Metal Gear when it was revealed the commander of Zanzibar Land was none other than Big Boss. The kinks, betrayals, and plot twists don't stop there, however. Soon, we find out the new Metal Gear, Metal Gear D, is piloted by his once friend and comrade, Gray Fox. Eventually, Solid Snake is confronted by Gray Fox in an ultimate showdown in a mine field, resulting in the death of Gray Fox. With his mission almost complete and without weapons of any sort, Solid Snake is confronted by Big Boss once more. In probably the greatest display of resourcefulness ever, Solid Snake takes on and defeats Big Boss with nothing more than a lighter and an aerosol can. Subsequently, Solid Snake retires to Alaska.

Metal Gear Solid: Solid Snake is brought out of retirement to infiltrate the facility in Shadow Moses after his former group, FOXHOUND, goes rogue under the command of Liquid Snake. Liquid and company demand the remains of Big Boss, and plan on using the newly built Metal Gear Rex to achieve the goal if their demands are not met. Solid Snake infiltrates the facility, rescuing Meryl Silverburgh and Hal Emmerich, aka Otacon. Solid Snake also meets Revolver Ocelot, who loses his arm to the Cyborg Ninja. The ninja turns out to be Gray Fox and allies himself with Solid Snake before the end. Ultimately, there is a final confrontation between Liquid and Solid Snake. Liquid reveals the truth about their origins; they are both clones of the legendary Big Boss. It is also revealed that Solid Snake was injected with a chemical compound, FOXDIE, but only as a carrier. It is speculated FOXDIE will eventually kill Solid Snake; the way it did the other member of FOXHOUND. Snake retires once more in Alaska, or so it would seem.

Metal Gear Solid 2: Sons of Liberty: Two years after the Shadow Moses incident, Solid Snake, in alliance with Otacon, seeks out newly developed models of Metal Gear in order to bring them down. Aboard the USS Discovery, a new Metal Gear is being carried in Manhattan Bay by the Marines. Solid Snake sneaks aboard the ship to obtain evidence of the weapon. However, Solid Snake was not the only one interested in the weapon. Sergei Gurlukovich, along with Ocelot and their own army, board the ship and slowly take it. After triggering explosives to sink the ship, Ocelot inadvertently reveals to Solid Snake that Liquid is still alive through him to the grafted arm that once belonged to Liquid. The events that followed two years later involved the kidnapping of the President and a new "Snake" entering the Big Shell. The new "Snake" is quickly re-codenamed Raiden. Raiden eventually discovers key information about the Philosophers and finds out Solid Snake was not dead. He then battles the "perfect" third clone of Big Boss, Solidus Snake. In the end, Raiden is victorious and parts ways with Solid Snake.